scitex 2.5.0__py3-none-any.whl → 2.7.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1091) hide show
  1. scitex/__init__.py +19 -8
  2. scitex/__main__.py +2 -1
  3. scitex/__version__.py +1 -1
  4. scitex/_optional_deps.py +13 -20
  5. scitex/ai/__init__.py +5 -0
  6. scitex/ai/_gen_ai/_Anthropic.py +3 -1
  7. scitex/ai/_gen_ai/_BaseGenAI.py +3 -2
  8. scitex/ai/_gen_ai/_DeepSeek.py +1 -1
  9. scitex/ai/_gen_ai/_Google.py +3 -2
  10. scitex/ai/_gen_ai/_Llama.py +4 -2
  11. scitex/ai/_gen_ai/_OpenAI.py +3 -1
  12. scitex/ai/_gen_ai/_PARAMS.py +1 -0
  13. scitex/ai/_gen_ai/_Perplexity.py +3 -1
  14. scitex/ai/_gen_ai/__init__.py +1 -0
  15. scitex/ai/_gen_ai/_format_output_func.py +3 -1
  16. scitex/ai/classification/CrossValidationExperiment.py +8 -14
  17. scitex/ai/classification/examples/timeseries_cv_demo.py +128 -112
  18. scitex/ai/classification/reporters/_BaseClassificationReporter.py +2 -0
  19. scitex/ai/classification/reporters/_ClassificationReporter.py +30 -45
  20. scitex/ai/classification/reporters/_MultiClassificationReporter.py +8 -11
  21. scitex/ai/classification/reporters/_SingleClassificationReporter.py +126 -182
  22. scitex/ai/classification/reporters/__init__.py +1 -1
  23. scitex/ai/classification/reporters/reporter_utils/_Plotter.py +213 -119
  24. scitex/ai/classification/reporters/reporter_utils/__init__.py +28 -36
  25. scitex/ai/classification/reporters/reporter_utils/aggregation.py +125 -143
  26. scitex/ai/classification/reporters/reporter_utils/data_models.py +128 -120
  27. scitex/ai/classification/reporters/reporter_utils/reporting.py +507 -340
  28. scitex/ai/classification/reporters/reporter_utils/storage.py +4 -1
  29. scitex/ai/classification/reporters/reporter_utils/validation.py +141 -154
  30. scitex/ai/classification/timeseries/_TimeSeriesBlockingSplit.py +204 -129
  31. scitex/ai/classification/timeseries/_TimeSeriesCalendarSplit.py +215 -171
  32. scitex/ai/classification/timeseries/_TimeSeriesMetadata.py +17 -17
  33. scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit.py +67 -143
  34. scitex/ai/classification/timeseries/_TimeSeriesSlidingWindowSplit_v01-not-using-n_splits.py +67 -143
  35. scitex/ai/classification/timeseries/_TimeSeriesStrategy.py +12 -13
  36. scitex/ai/classification/timeseries/_TimeSeriesStratifiedSplit.py +231 -144
  37. scitex/ai/classification/timeseries/__init__.py +2 -4
  38. scitex/ai/classification/timeseries/_normalize_timestamp.py +3 -0
  39. scitex/ai/clustering/_pca.py +0 -1
  40. scitex/ai/clustering/_umap.py +1 -2
  41. scitex/ai/feature_extraction/__init__.py +10 -8
  42. scitex/ai/feature_extraction/vit.py +0 -1
  43. scitex/ai/feature_selection/feature_selection.py +3 -8
  44. scitex/ai/metrics/_calc_conf_mat.py +2 -0
  45. scitex/ai/metrics/_calc_feature_importance.py +3 -7
  46. scitex/ai/metrics/_calc_pre_rec_auc.py +5 -5
  47. scitex/ai/metrics/_calc_roc_auc.py +4 -2
  48. scitex/ai/metrics/_calc_seizure_prediction_metrics.py +35 -20
  49. scitex/ai/metrics/_calc_silhouette_score.py +1 -3
  50. scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger.py +0 -3
  51. scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger2020.py +0 -3
  52. scitex/ai/optim/Ranger_Deep_Learning_Optimizer/ranger/ranger913A.py +0 -3
  53. scitex/ai/optim/_optimizers.py +1 -1
  54. scitex/ai/plt/__init__.py +6 -1
  55. scitex/ai/plt/_plot_feature_importance.py +1 -3
  56. scitex/ai/plt/_plot_learning_curve.py +9 -24
  57. scitex/ai/plt/_plot_optuna_study.py +4 -3
  58. scitex/ai/plt/_plot_pre_rec_curve.py +9 -15
  59. scitex/ai/plt/_plot_roc_curve.py +6 -8
  60. scitex/ai/plt/_stx_conf_mat.py +121 -122
  61. scitex/ai/sampling/undersample.py +3 -2
  62. scitex/ai/sklearn/__init__.py +2 -2
  63. scitex/ai/training/_LearningCurveLogger.py +23 -10
  64. scitex/ai/utils/_check_params.py +0 -1
  65. scitex/benchmark/__init__.py +15 -25
  66. scitex/benchmark/benchmark.py +124 -117
  67. scitex/benchmark/monitor.py +117 -107
  68. scitex/benchmark/profiler.py +61 -58
  69. scitex/bridge/__init__.py +110 -0
  70. scitex/bridge/_helpers.py +149 -0
  71. scitex/bridge/_plt_vis.py +529 -0
  72. scitex/bridge/_protocol.py +283 -0
  73. scitex/bridge/_stats_plt.py +261 -0
  74. scitex/bridge/_stats_vis.py +265 -0
  75. scitex/browser/__init__.py +0 -2
  76. scitex/browser/auth/__init__.py +0 -0
  77. scitex/browser/auth/google.py +16 -11
  78. scitex/browser/automation/CookieHandler.py +2 -3
  79. scitex/browser/collaboration/__init__.py +3 -0
  80. scitex/browser/collaboration/auth_helpers.py +3 -1
  81. scitex/browser/collaboration/collaborative_agent.py +2 -0
  82. scitex/browser/collaboration/interactive_panel.py +2 -2
  83. scitex/browser/collaboration/shared_session.py +20 -11
  84. scitex/browser/collaboration/standard_interactions.py +1 -0
  85. scitex/browser/core/BrowserMixin.py +12 -30
  86. scitex/browser/core/ChromeProfileManager.py +9 -24
  87. scitex/browser/debugging/_browser_logger.py +15 -25
  88. scitex/browser/debugging/_failure_capture.py +9 -2
  89. scitex/browser/debugging/_highlight_element.py +15 -6
  90. scitex/browser/debugging/_show_grid.py +5 -6
  91. scitex/browser/debugging/_sync_session.py +4 -3
  92. scitex/browser/debugging/_test_monitor.py +14 -5
  93. scitex/browser/debugging/_visual_cursor.py +46 -35
  94. scitex/browser/interaction/click_center.py +4 -3
  95. scitex/browser/interaction/click_with_fallbacks.py +7 -10
  96. scitex/browser/interaction/close_popups.py +79 -66
  97. scitex/browser/interaction/fill_with_fallbacks.py +8 -8
  98. scitex/browser/pdf/__init__.py +3 -1
  99. scitex/browser/pdf/click_download_for_chrome_pdf_viewer.py +11 -10
  100. scitex/browser/pdf/detect_chrome_pdf_viewer.py +3 -6
  101. scitex/browser/remote/CaptchaHandler.py +109 -96
  102. scitex/browser/remote/ZenRowsAPIClient.py +91 -97
  103. scitex/browser/remote/ZenRowsBrowserManager.py +138 -112
  104. scitex/browser/stealth/HumanBehavior.py +4 -9
  105. scitex/browser/stealth/StealthManager.py +11 -26
  106. scitex/capture/__init__.py +17 -17
  107. scitex/capture/__main__.py +2 -3
  108. scitex/capture/capture.py +23 -51
  109. scitex/capture/cli.py +14 -39
  110. scitex/capture/gif.py +5 -9
  111. scitex/capture/mcp_server.py +7 -20
  112. scitex/capture/session.py +4 -3
  113. scitex/capture/utils.py +18 -53
  114. scitex/cli/__init__.py +1 -1
  115. scitex/cli/cloud.py +158 -116
  116. scitex/cli/config.py +224 -0
  117. scitex/cli/main.py +41 -40
  118. scitex/cli/scholar.py +60 -27
  119. scitex/cli/security.py +14 -20
  120. scitex/cli/web.py +87 -90
  121. scitex/cli/writer.py +51 -45
  122. scitex/cloud/__init__.py +14 -11
  123. scitex/cloud/_matplotlib_hook.py +6 -6
  124. scitex/config/README.md +313 -0
  125. scitex/config/{PriorityConfig.py → _PriorityConfig.py} +114 -17
  126. scitex/config/_ScitexConfig.py +319 -0
  127. scitex/config/__init__.py +41 -9
  128. scitex/config/_paths.py +325 -0
  129. scitex/config/default.yaml +81 -0
  130. scitex/context/_suppress_output.py +2 -3
  131. scitex/db/_BaseMixins/_BaseBackupMixin.py +3 -1
  132. scitex/db/_BaseMixins/_BaseBatchMixin.py +3 -1
  133. scitex/db/_BaseMixins/_BaseBlobMixin.py +3 -1
  134. scitex/db/_BaseMixins/_BaseImportExportMixin.py +1 -3
  135. scitex/db/_BaseMixins/_BaseIndexMixin.py +3 -1
  136. scitex/db/_BaseMixins/_BaseMaintenanceMixin.py +1 -3
  137. scitex/db/_BaseMixins/_BaseQueryMixin.py +3 -1
  138. scitex/db/_BaseMixins/_BaseRowMixin.py +3 -1
  139. scitex/db/_BaseMixins/_BaseTableMixin.py +3 -1
  140. scitex/db/_BaseMixins/_BaseTransactionMixin.py +1 -3
  141. scitex/db/_BaseMixins/__init__.py +1 -1
  142. scitex/db/__init__.py +9 -1
  143. scitex/db/__main__.py +8 -21
  144. scitex/db/_check_health.py +15 -31
  145. scitex/db/_delete_duplicates.py +7 -4
  146. scitex/db/_inspect.py +22 -38
  147. scitex/db/_inspect_optimized.py +89 -85
  148. scitex/db/_postgresql/_PostgreSQL.py +0 -1
  149. scitex/db/_postgresql/_PostgreSQLMixins/_BlobMixin.py +3 -1
  150. scitex/db/_postgresql/_PostgreSQLMixins/_ConnectionMixin.py +1 -3
  151. scitex/db/_postgresql/_PostgreSQLMixins/_ImportExportMixin.py +1 -3
  152. scitex/db/_postgresql/_PostgreSQLMixins/_MaintenanceMixin.py +1 -4
  153. scitex/db/_postgresql/_PostgreSQLMixins/_QueryMixin.py +3 -3
  154. scitex/db/_postgresql/_PostgreSQLMixins/_RowMixin.py +3 -1
  155. scitex/db/_postgresql/_PostgreSQLMixins/_TransactionMixin.py +1 -3
  156. scitex/db/_postgresql/__init__.py +1 -1
  157. scitex/db/_sqlite3/_SQLite3.py +2 -4
  158. scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin.py +11 -12
  159. scitex/db/_sqlite3/_SQLite3Mixins/_ArrayMixin_v01-need-_hash-col.py +19 -14
  160. scitex/db/_sqlite3/_SQLite3Mixins/_BatchMixin.py +3 -1
  161. scitex/db/_sqlite3/_SQLite3Mixins/_BlobMixin.py +7 -7
  162. scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin.py +118 -111
  163. scitex/db/_sqlite3/_SQLite3Mixins/_ConnectionMixin.py +8 -10
  164. scitex/db/_sqlite3/_SQLite3Mixins/_GitMixin.py +17 -45
  165. scitex/db/_sqlite3/_SQLite3Mixins/_ImportExportMixin.py +1 -3
  166. scitex/db/_sqlite3/_SQLite3Mixins/_IndexMixin.py +3 -1
  167. scitex/db/_sqlite3/_SQLite3Mixins/_QueryMixin.py +3 -4
  168. scitex/db/_sqlite3/_SQLite3Mixins/_RowMixin.py +9 -9
  169. scitex/db/_sqlite3/_SQLite3Mixins/_TableMixin.py +18 -11
  170. scitex/db/_sqlite3/_SQLite3Mixins/__init__.py +1 -0
  171. scitex/db/_sqlite3/__init__.py +1 -1
  172. scitex/db/_sqlite3/_delete_duplicates.py +13 -11
  173. scitex/decorators/__init__.py +29 -4
  174. scitex/decorators/_auto_order.py +43 -43
  175. scitex/decorators/_batch_fn.py +12 -6
  176. scitex/decorators/_cache_disk.py +8 -9
  177. scitex/decorators/_cache_disk_async.py +8 -7
  178. scitex/decorators/_combined.py +19 -13
  179. scitex/decorators/_converters.py +16 -3
  180. scitex/decorators/_deprecated.py +32 -22
  181. scitex/decorators/_numpy_fn.py +18 -4
  182. scitex/decorators/_pandas_fn.py +17 -5
  183. scitex/decorators/_signal_fn.py +17 -3
  184. scitex/decorators/_torch_fn.py +32 -15
  185. scitex/decorators/_xarray_fn.py +23 -9
  186. scitex/dev/_analyze_code_flow.py +0 -2
  187. scitex/dict/_DotDict.py +15 -19
  188. scitex/dict/_flatten.py +1 -0
  189. scitex/dict/_listed_dict.py +1 -0
  190. scitex/dict/_pop_keys.py +1 -0
  191. scitex/dict/_replace.py +1 -0
  192. scitex/dict/_safe_merge.py +1 -0
  193. scitex/dict/_to_str.py +2 -3
  194. scitex/dsp/__init__.py +13 -4
  195. scitex/dsp/_crop.py +3 -1
  196. scitex/dsp/_detect_ripples.py +3 -1
  197. scitex/dsp/_modulation_index.py +3 -1
  198. scitex/dsp/_time.py +3 -1
  199. scitex/dsp/_wavelet.py +0 -1
  200. scitex/dsp/example.py +0 -5
  201. scitex/dsp/filt.py +4 -0
  202. scitex/dsp/utils/__init__.py +4 -1
  203. scitex/dsp/utils/pac.py +3 -3
  204. scitex/dt/_normalize_timestamp.py +4 -1
  205. scitex/errors.py +3 -6
  206. scitex/etc/__init__.py +1 -1
  207. scitex/gen/_DimHandler.py +6 -6
  208. scitex/gen/__init__.py +5 -1
  209. scitex/gen/_deprecated_close.py +1 -0
  210. scitex/gen/_deprecated_start.py +5 -3
  211. scitex/gen/_detect_environment.py +44 -41
  212. scitex/gen/_detect_notebook_path.py +51 -47
  213. scitex/gen/_embed.py +1 -1
  214. scitex/gen/_get_notebook_path.py +81 -62
  215. scitex/gen/_inspect_module.py +0 -1
  216. scitex/gen/_norm.py +16 -7
  217. scitex/gen/_norm_cache.py +78 -65
  218. scitex/gen/_print_config.py +0 -3
  219. scitex/gen/_src.py +2 -3
  220. scitex/gen/_title_case.py +3 -2
  221. scitex/gen/_to_even.py +8 -8
  222. scitex/gen/_transpose.py +3 -3
  223. scitex/gen/misc.py +0 -3
  224. scitex/gists/_SigMacro_processFigure_S.py +2 -2
  225. scitex/gists/_SigMacro_toBlue.py +2 -2
  226. scitex/gists/__init__.py +4 -1
  227. scitex/git/_branch.py +19 -11
  228. scitex/git/_clone.py +23 -15
  229. scitex/git/_commit.py +10 -12
  230. scitex/git/_init.py +15 -38
  231. scitex/git/_remote.py +9 -3
  232. scitex/git/_result.py +3 -0
  233. scitex/git/_retry.py +2 -5
  234. scitex/git/_types.py +4 -0
  235. scitex/git/_validation.py +8 -8
  236. scitex/git/_workflow.py +4 -4
  237. scitex/io/__init__.py +2 -1
  238. scitex/io/_glob.py +2 -2
  239. scitex/io/_json2md.py +3 -3
  240. scitex/io/_load.py +6 -8
  241. scitex/io/_load_cache.py +71 -71
  242. scitex/io/_load_configs.py +2 -3
  243. scitex/io/_load_modules/_H5Explorer.py +6 -12
  244. scitex/io/_load_modules/_ZarrExplorer.py +3 -3
  245. scitex/io/_load_modules/_bibtex.py +62 -63
  246. scitex/io/_load_modules/_canvas.py +4 -9
  247. scitex/io/_load_modules/_catboost.py +7 -2
  248. scitex/io/_load_modules/_hdf5.py +2 -0
  249. scitex/io/_load_modules/_image.py +5 -1
  250. scitex/io/_load_modules/_matlab.py +3 -1
  251. scitex/io/_load_modules/_optuna.py +0 -1
  252. scitex/io/_load_modules/_pdf.py +38 -29
  253. scitex/io/_load_modules/_sqlite3.py +1 -0
  254. scitex/io/_load_modules/_txt.py +2 -0
  255. scitex/io/_load_modules/_xml.py +9 -9
  256. scitex/io/_load_modules/_zarr.py +12 -10
  257. scitex/io/_metadata.py +76 -37
  258. scitex/io/_qr_utils.py +18 -13
  259. scitex/io/_save.py +220 -63
  260. scitex/io/_save_modules/__init__.py +7 -2
  261. scitex/io/_save_modules/_bibtex.py +66 -61
  262. scitex/io/_save_modules/_canvas.py +5 -6
  263. scitex/io/_save_modules/_catboost.py +2 -2
  264. scitex/io/_save_modules/_csv.py +4 -4
  265. scitex/io/_save_modules/_excel.py +5 -9
  266. scitex/io/_save_modules/_hdf5.py +9 -21
  267. scitex/io/_save_modules/_html.py +5 -5
  268. scitex/io/_save_modules/_image.py +105 -8
  269. scitex/io/_save_modules/_joblib.py +2 -2
  270. scitex/io/_save_modules/_json.py +51 -6
  271. scitex/io/_save_modules/_listed_dfs_as_csv.py +2 -1
  272. scitex/io/_save_modules/_listed_scalars_as_csv.py +2 -1
  273. scitex/io/_save_modules/_matlab.py +2 -2
  274. scitex/io/_save_modules/_numpy.py +6 -8
  275. scitex/io/_save_modules/_pickle.py +4 -4
  276. scitex/io/_save_modules/_plotly.py +3 -3
  277. scitex/io/_save_modules/_tex.py +23 -25
  278. scitex/io/_save_modules/_text.py +2 -2
  279. scitex/io/_save_modules/_yaml.py +9 -9
  280. scitex/io/_save_modules/_zarr.py +15 -15
  281. scitex/io/utils/__init__.py +2 -1
  282. scitex/io/utils/h5_to_zarr.py +173 -155
  283. scitex/linalg/__init__.py +1 -1
  284. scitex/linalg/_geometric_median.py +4 -3
  285. scitex/logging/_Tee.py +5 -7
  286. scitex/logging/__init__.py +18 -19
  287. scitex/logging/_config.py +4 -1
  288. scitex/logging/_context.py +6 -5
  289. scitex/logging/_formatters.py +2 -3
  290. scitex/logging/_handlers.py +19 -20
  291. scitex/logging/_levels.py +9 -17
  292. scitex/logging/_logger.py +74 -15
  293. scitex/logging/_print_capture.py +17 -17
  294. scitex/nn/_BNet.py +1 -3
  295. scitex/nn/_Filters.py +6 -2
  296. scitex/nn/_ModulationIndex.py +3 -1
  297. scitex/nn/_PAC.py +3 -2
  298. scitex/nn/_PSD.py +0 -1
  299. scitex/nn/__init__.py +16 -3
  300. scitex/path/_clean.py +10 -8
  301. scitex/path/_find.py +1 -1
  302. scitex/path/_get_spath.py +1 -2
  303. scitex/path/_mk_spath.py +1 -1
  304. scitex/path/_symlink.py +5 -10
  305. scitex/pd/__init__.py +4 -1
  306. scitex/pd/_force_df.py +24 -24
  307. scitex/pd/_get_unique.py +1 -0
  308. scitex/pd/_merge_columns.py +1 -1
  309. scitex/pd/_round.py +11 -7
  310. scitex/pd/_to_xy.py +0 -1
  311. scitex/plt/REQUESTS.md +191 -0
  312. scitex/plt/__init__.py +185 -87
  313. scitex/plt/_subplots/_AxesWrapper.py +22 -6
  314. scitex/plt/_subplots/_AxisWrapper.py +100 -39
  315. scitex/plt/_subplots/_AxisWrapperMixins/_AdjustmentMixin.py +74 -52
  316. scitex/plt/_subplots/_AxisWrapperMixins/_MatplotlibPlotMixin.py +183 -73
  317. scitex/plt/_subplots/_AxisWrapperMixins/_SeabornMixin.py +61 -45
  318. scitex/plt/_subplots/_AxisWrapperMixins/_TrackingMixin.py +26 -14
  319. scitex/plt/_subplots/_AxisWrapperMixins/_UnitAwareMixin.py +80 -73
  320. scitex/plt/_subplots/_FigWrapper.py +93 -60
  321. scitex/plt/_subplots/_SubplotsWrapper.py +135 -68
  322. scitex/plt/_subplots/__init__.py +10 -0
  323. scitex/plt/_subplots/_export_as_csv.py +89 -47
  324. scitex/plt/_subplots/_export_as_csv_formatters/__init__.py +1 -0
  325. scitex/plt/_subplots/_export_as_csv_formatters/_format_annotate.py +6 -4
  326. scitex/plt/_subplots/_export_as_csv_formatters/_format_bar.py +88 -38
  327. scitex/plt/_subplots/_export_as_csv_formatters/_format_barh.py +25 -31
  328. scitex/plt/_subplots/_export_as_csv_formatters/_format_boxplot.py +53 -23
  329. scitex/plt/_subplots/_export_as_csv_formatters/_format_contour.py +38 -25
  330. scitex/plt/_subplots/_export_as_csv_formatters/_format_contourf.py +17 -9
  331. scitex/plt/_subplots/_export_as_csv_formatters/_format_errorbar.py +70 -124
  332. scitex/plt/_subplots/_export_as_csv_formatters/_format_eventplot.py +12 -10
  333. scitex/plt/_subplots/_export_as_csv_formatters/_format_fill.py +31 -17
  334. scitex/plt/_subplots/_export_as_csv_formatters/_format_fill_between.py +33 -21
  335. scitex/plt/_subplots/_export_as_csv_formatters/_format_hexbin.py +14 -4
  336. scitex/plt/_subplots/_export_as_csv_formatters/_format_hist.py +43 -29
  337. scitex/plt/_subplots/_export_as_csv_formatters/_format_hist2d.py +14 -4
  338. scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow.py +27 -11
  339. scitex/plt/_subplots/_export_as_csv_formatters/_format_imshow2d.py +7 -5
  340. scitex/plt/_subplots/_export_as_csv_formatters/_format_matshow.py +9 -7
  341. scitex/plt/_subplots/_export_as_csv_formatters/_format_pie.py +15 -6
  342. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot.py +85 -46
  343. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_box.py +52 -27
  344. scitex/plt/_subplots/_export_as_csv_formatters/_format_plot_imshow.py +1 -0
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  891. scitex/scholar/url_finder/translators/individual/sciencedirect.py +36 -17
  892. scitex/scholar/url_finder/translators/individual/semantics_visual_library.py +3 -1
  893. scitex/scholar/url_finder/translators/individual/silverchair.py +70 -52
  894. scitex/scholar/url_finder/translators/individual/sora.py +3 -1
  895. scitex/scholar/url_finder/translators/individual/springer.py +15 -11
  896. scitex/scholar/url_finder/translators/individual/ssrn.py +3 -3
  897. scitex/scholar/url_finder/translators/individual/stanford_encyclopedia_of_philosophy.py +3 -1
  898. scitex/scholar/url_finder/translators/individual/superlib.py +3 -1
  899. scitex/scholar/url_finder/translators/individual/treesearch.py +3 -1
  900. scitex/scholar/url_finder/translators/individual/university_of_chicago_press_books.py +3 -1
  901. scitex/scholar/url_finder/translators/individual/vlex.py +3 -1
  902. scitex/scholar/url_finder/translators/individual/web_of_science.py +3 -1
  903. scitex/scholar/url_finder/translators/individual/web_of_science_nextgen.py +3 -1
  904. scitex/scholar/url_finder/translators/individual/wiley.py +31 -25
  905. scitex/scholar/url_finder/translators/individual/wilson_center_digital_archive.py +3 -1
  906. scitex/scholar/utils/bibtex/_parse_bibtex.py +3 -3
  907. scitex/scholar/utils/cleanup/_cleanup_scholar_processes.py +5 -9
  908. scitex/scholar/utils/text/_TextNormalizer.py +249 -176
  909. scitex/scholar/utils/validation/DOIValidator.py +31 -28
  910. scitex/scholar/utils/validation/__init__.py +0 -0
  911. scitex/scholar/utils/validation/validate_library_dois.py +61 -57
  912. scitex/scholar/zotero/__init__.py +1 -1
  913. scitex/security/cli.py +7 -20
  914. scitex/security/github.py +45 -32
  915. scitex/session/__init__.py +8 -9
  916. scitex/session/_decorator.py +49 -42
  917. scitex/session/_lifecycle.py +39 -39
  918. scitex/session/_manager.py +24 -20
  919. scitex/sh/__init__.py +4 -3
  920. scitex/sh/_execute.py +10 -7
  921. scitex/sh/_security.py +3 -3
  922. scitex/sh/_types.py +2 -3
  923. scitex/stats/__init__.py +57 -6
  924. scitex/stats/_schema.py +42 -569
  925. scitex/stats/auto/__init__.py +188 -0
  926. scitex/stats/auto/_context.py +331 -0
  927. scitex/stats/auto/_formatting.py +679 -0
  928. scitex/stats/auto/_rules.py +901 -0
  929. scitex/stats/auto/_selector.py +554 -0
  930. scitex/stats/auto/_styles.py +721 -0
  931. scitex/stats/correct/__init__.py +4 -4
  932. scitex/stats/correct/_correct_bonferroni.py +43 -34
  933. scitex/stats/correct/_correct_fdr.py +14 -40
  934. scitex/stats/correct/_correct_fdr_.py +39 -46
  935. scitex/stats/correct/_correct_holm.py +14 -32
  936. scitex/stats/correct/_correct_sidak.py +36 -21
  937. scitex/stats/descriptive/_circular.py +20 -21
  938. scitex/stats/descriptive/_describe.py +19 -5
  939. scitex/stats/descriptive/_nan.py +5 -7
  940. scitex/stats/descriptive/_real.py +4 -3
  941. scitex/stats/effect_sizes/__init__.py +10 -11
  942. scitex/stats/effect_sizes/_cliffs_delta.py +35 -32
  943. scitex/stats/effect_sizes/_cohens_d.py +30 -31
  944. scitex/stats/effect_sizes/_epsilon_squared.py +19 -22
  945. scitex/stats/effect_sizes/_eta_squared.py +23 -27
  946. scitex/stats/effect_sizes/_prob_superiority.py +18 -21
  947. scitex/stats/posthoc/__init__.py +3 -3
  948. scitex/stats/posthoc/_dunnett.py +75 -55
  949. scitex/stats/posthoc/_games_howell.py +61 -43
  950. scitex/stats/posthoc/_tukey_hsd.py +42 -34
  951. scitex/stats/power/__init__.py +2 -2
  952. scitex/stats/power/_power.py +56 -56
  953. scitex/stats/tests/__init__.py +1 -1
  954. scitex/stats/tests/correlation/__init__.py +1 -1
  955. scitex/stats/tests/correlation/_test_pearson.py +28 -38
  956. scitex/stats/utils/__init__.py +14 -17
  957. scitex/stats/utils/_effect_size.py +85 -78
  958. scitex/stats/utils/_formatters.py +49 -43
  959. scitex/stats/utils/_normalizers.py +7 -14
  960. scitex/stats/utils/_power.py +56 -56
  961. scitex/str/__init__.py +1 -0
  962. scitex/str/_clean_path.py +3 -3
  963. scitex/str/_factor_out_digits.py +86 -58
  964. scitex/str/_format_plot_text.py +180 -111
  965. scitex/str/_latex.py +19 -19
  966. scitex/str/_latex_fallback.py +9 -10
  967. scitex/str/_parse.py +3 -6
  968. scitex/str/_print_debug.py +13 -13
  969. scitex/str/_printc.py +2 -0
  970. scitex/str/_search.py +3 -3
  971. scitex/template/.legacy/_clone_project.py +9 -13
  972. scitex/template/__init__.py +10 -2
  973. scitex/template/_clone_project.py +7 -2
  974. scitex/template/_copy.py +1 -0
  975. scitex/template/_customize.py +3 -6
  976. scitex/template/_git_strategy.py +2 -3
  977. scitex/template/_rename.py +1 -0
  978. scitex/template/clone_pip_project.py +6 -7
  979. scitex/template/clone_research.py +7 -10
  980. scitex/template/clone_singularity.py +6 -7
  981. scitex/template/clone_writer_directory.py +6 -7
  982. scitex/tex/_preview.py +26 -11
  983. scitex/tex/_to_vec.py +10 -7
  984. scitex/torch/__init__.py +11 -1
  985. scitex/types/_ArrayLike.py +2 -0
  986. scitex/types/_is_listed_X.py +3 -3
  987. scitex/units.py +110 -77
  988. scitex/utils/_compress_hdf5.py +3 -3
  989. scitex/utils/_email.py +8 -4
  990. scitex/utils/_notify.py +14 -8
  991. scitex/utils/_search.py +6 -6
  992. scitex/utils/_verify_scitex_format.py +17 -42
  993. scitex/utils/_verify_scitex_format_v01.py +12 -34
  994. scitex/utils/template.py +4 -3
  995. scitex/vis/__init__.py +0 -0
  996. scitex/vis/backend/__init__.py +3 -3
  997. scitex/vis/backend/{export.py → _export.py} +1 -1
  998. scitex/vis/backend/{parser.py → _parser.py} +1 -3
  999. scitex/vis/backend/{render.py → _render.py} +1 -1
  1000. scitex/vis/canvas.py +15 -3
  1001. scitex/vis/editor/__init__.py +0 -0
  1002. scitex/vis/editor/_dearpygui_editor.py +450 -304
  1003. scitex/vis/editor/_defaults.py +114 -123
  1004. scitex/vis/editor/_edit.py +38 -26
  1005. scitex/vis/editor/_flask_editor.py +8 -8
  1006. scitex/vis/editor/_mpl_editor.py +63 -48
  1007. scitex/vis/editor/_qt_editor.py +210 -159
  1008. scitex/vis/editor/_tkinter_editor.py +146 -89
  1009. scitex/vis/editor/flask_editor/__init__.py +10 -10
  1010. scitex/vis/editor/flask_editor/_bbox.py +529 -0
  1011. scitex/vis/editor/flask_editor/{core.py → _core.py} +45 -29
  1012. scitex/vis/editor/flask_editor/_plotter.py +567 -0
  1013. scitex/vis/editor/flask_editor/_renderer.py +393 -0
  1014. scitex/vis/editor/flask_editor/{utils.py → _utils.py} +13 -14
  1015. scitex/vis/editor/flask_editor/templates/__init__.py +5 -5
  1016. scitex/vis/editor/flask_editor/templates/{html.py → _html.py} +234 -16
  1017. scitex/vis/editor/flask_editor/templates/_scripts.py +1261 -0
  1018. scitex/vis/editor/flask_editor/templates/{styles.py → _styles.py} +192 -2
  1019. scitex/vis/io/__init__.py +5 -5
  1020. scitex/vis/io/{canvas.py → _canvas.py} +8 -4
  1021. scitex/vis/io/{data.py → _data.py} +13 -9
  1022. scitex/vis/io/{directory.py → _directory.py} +7 -4
  1023. scitex/vis/io/{export.py → _export.py} +15 -12
  1024. scitex/vis/io/{load.py → _load.py} +1 -1
  1025. scitex/vis/io/{panel.py → _panel.py} +21 -13
  1026. scitex/vis/io/{save.py → _save.py} +0 -0
  1027. scitex/vis/model/__init__.py +7 -7
  1028. scitex/vis/model/{annotations.py → _annotations.py} +2 -4
  1029. scitex/vis/model/{axes.py → _axes.py} +1 -1
  1030. scitex/vis/model/{figure.py → _figure.py} +0 -0
  1031. scitex/vis/model/{guides.py → _guides.py} +1 -1
  1032. scitex/vis/model/{plot.py → _plot.py} +2 -4
  1033. scitex/vis/model/{plot_types.py → _plot_types.py} +0 -0
  1034. scitex/vis/model/{styles.py → _styles.py} +0 -0
  1035. scitex/vis/utils/__init__.py +2 -2
  1036. scitex/vis/utils/{defaults.py → _defaults.py} +1 -2
  1037. scitex/vis/utils/{validate.py → _validate.py} +3 -9
  1038. scitex/web/__init__.py +7 -1
  1039. scitex/web/_scraping.py +54 -38
  1040. scitex/web/_search_pubmed.py +30 -14
  1041. scitex/writer/.legacy/Writer_v01-refactored.py +4 -4
  1042. scitex/writer/.legacy/_compile.py +18 -28
  1043. scitex/writer/Writer.py +8 -21
  1044. scitex/writer/__init__.py +11 -11
  1045. scitex/writer/_clone_writer_project.py +2 -6
  1046. scitex/writer/_compile/__init__.py +1 -0
  1047. scitex/writer/_compile/_parser.py +1 -0
  1048. scitex/writer/_compile/_runner.py +35 -38
  1049. scitex/writer/_compile/_validator.py +1 -0
  1050. scitex/writer/_compile/manuscript.py +1 -0
  1051. scitex/writer/_compile/revision.py +1 -0
  1052. scitex/writer/_compile/supplementary.py +1 -0
  1053. scitex/writer/_compile_async.py +5 -12
  1054. scitex/writer/_project/__init__.py +1 -0
  1055. scitex/writer/_project/_create.py +10 -25
  1056. scitex/writer/_project/_trees.py +4 -9
  1057. scitex/writer/_project/_validate.py +2 -3
  1058. scitex/writer/_validate_tree_structures.py +7 -18
  1059. scitex/writer/dataclasses/__init__.py +8 -10
  1060. scitex/writer/dataclasses/config/_CONSTANTS.py +2 -3
  1061. scitex/writer/dataclasses/config/_WriterConfig.py +4 -9
  1062. scitex/writer/dataclasses/contents/_ManuscriptContents.py +14 -25
  1063. scitex/writer/dataclasses/contents/_RevisionContents.py +21 -16
  1064. scitex/writer/dataclasses/contents/_SupplementaryContents.py +21 -24
  1065. scitex/writer/dataclasses/core/_Document.py +2 -3
  1066. scitex/writer/dataclasses/core/_DocumentSection.py +8 -23
  1067. scitex/writer/dataclasses/results/_CompilationResult.py +2 -3
  1068. scitex/writer/dataclasses/results/_LaTeXIssue.py +3 -6
  1069. scitex/writer/dataclasses/results/_SaveSectionsResponse.py +20 -9
  1070. scitex/writer/dataclasses/results/_SectionReadResponse.py +24 -10
  1071. scitex/writer/dataclasses/tree/_ConfigTree.py +7 -4
  1072. scitex/writer/dataclasses/tree/_ManuscriptTree.py +10 -13
  1073. scitex/writer/dataclasses/tree/_RevisionTree.py +16 -17
  1074. scitex/writer/dataclasses/tree/_ScriptsTree.py +10 -5
  1075. scitex/writer/dataclasses/tree/_SharedTree.py +10 -13
  1076. scitex/writer/dataclasses/tree/_SupplementaryTree.py +15 -14
  1077. scitex/writer/utils/.legacy_git_retry.py +3 -8
  1078. scitex/writer/utils/_parse_latex_logs.py +2 -3
  1079. scitex/writer/utils/_parse_script_args.py +20 -23
  1080. scitex/writer/utils/_watch.py +5 -5
  1081. {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/METADATA +4 -10
  1082. {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/RECORD +1071 -975
  1083. scitex/db/_sqlite3/_SQLite3Mixins/_ColumnMixin_v01-indentation-issues.py +0 -583
  1084. scitex/plt/_subplots/_export_as_csv_formatters.py +0 -112
  1085. scitex/vis/editor/flask_editor/bbox.py +0 -216
  1086. scitex/vis/editor/flask_editor/plotter.py +0 -130
  1087. scitex/vis/editor/flask_editor/renderer.py +0 -184
  1088. scitex/vis/editor/flask_editor/templates/scripts.py +0 -614
  1089. {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/WHEEL +0 -0
  1090. {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/entry_points.txt +0 -0
  1091. {scitex-2.5.0.dist-info → scitex-2.7.0.dist-info}/licenses/LICENSE +0 -0
scitex/cli/web.py CHANGED
@@ -45,25 +45,25 @@ def web():
45
45
 
46
46
 
47
47
  @web.command()
48
- @click.argument('url')
48
+ @click.argument("url")
49
49
  @click.option(
50
- '--pattern', '-p',
51
- help='Regex pattern to filter URLs (e.g., "\\.pdf$" for PDF files)'
50
+ "--pattern",
51
+ "-p",
52
+ help='Regex pattern to filter URLs (e.g., "\\.pdf$" for PDF files)',
52
53
  )
53
54
  @click.option(
54
- '--same-domain',
55
- is_flag=True,
56
- help='Only include URLs from the same domain'
55
+ "--same-domain", is_flag=True, help="Only include URLs from the same domain"
57
56
  )
58
57
  @click.option(
59
- '--relative',
58
+ "--relative",
60
59
  is_flag=True,
61
- help='Keep URLs as relative instead of converting to absolute'
60
+ help="Keep URLs as relative instead of converting to absolute",
62
61
  )
63
62
  @click.option(
64
- '--output', '-o',
63
+ "--output",
64
+ "-o",
65
65
  type=click.Path(),
66
- help='Save URLs to file instead of printing to stdout'
66
+ help="Save URLs to file instead of printing to stdout",
67
67
  )
68
68
  def get_urls_cmd(url, pattern, same_domain, relative, output):
69
69
  """Extract all URLs from a webpage."""
@@ -71,23 +71,20 @@ def get_urls_cmd(url, pattern, same_domain, relative, output):
71
71
  click.echo(f"Extracting URLs from: {url}")
72
72
 
73
73
  urls = get_urls(
74
- url,
75
- pattern=pattern,
76
- absolute=not relative,
77
- same_domain=same_domain
74
+ url, pattern=pattern, absolute=not relative, same_domain=same_domain
78
75
  )
79
76
 
80
77
  if not urls:
81
- click.secho("No URLs found", fg='yellow')
78
+ click.secho("No URLs found", fg="yellow")
82
79
  sys.exit(0)
83
80
 
84
- click.secho(f"Found {len(urls)} URLs", fg='green')
81
+ click.secho(f"Found {len(urls)} URLs", fg="green")
85
82
 
86
83
  if output:
87
84
  output_path = Path(output)
88
85
  output_path.parent.mkdir(parents=True, exist_ok=True)
89
- with open(output_path, 'w') as f:
90
- f.write('\n'.join(urls))
86
+ with open(output_path, "w") as f:
87
+ f.write("\n".join(urls))
91
88
  click.echo(f"URLs saved to: {output_path}")
92
89
  else:
93
90
  click.echo()
@@ -97,48 +94,42 @@ def get_urls_cmd(url, pattern, same_domain, relative, output):
97
94
  sys.exit(0)
98
95
 
99
96
  except Exception as e:
100
- click.secho(f"ERROR: {e}", fg='red', err=True)
97
+ click.secho(f"ERROR: {e}", fg="red", err=True)
101
98
  sys.exit(1)
102
99
 
103
100
 
104
101
  @web.command()
105
- @click.argument('url')
102
+ @click.argument("url")
106
103
  @click.option(
107
- '--pattern', '-p',
108
- help='Regex pattern to filter image URLs (e.g., "\\.jpg$")'
104
+ "--pattern", "-p", help='Regex pattern to filter image URLs (e.g., "\\.jpg$")'
109
105
  )
110
106
  @click.option(
111
- '--same-domain',
112
- is_flag=True,
113
- help='Only include images from the same domain'
107
+ "--same-domain", is_flag=True, help="Only include images from the same domain"
114
108
  )
115
109
  @click.option(
116
- '--output', '-o',
110
+ "--output",
111
+ "-o",
117
112
  type=click.Path(),
118
- help='Save image URLs to file instead of printing to stdout'
113
+ help="Save image URLs to file instead of printing to stdout",
119
114
  )
120
115
  def get_image_urls_cmd(url, pattern, same_domain, output):
121
116
  """Extract image URLs from a webpage without downloading them."""
122
117
  try:
123
118
  click.echo(f"Extracting image URLs from: {url}")
124
119
 
125
- img_urls = get_image_urls(
126
- url,
127
- pattern=pattern,
128
- same_domain=same_domain
129
- )
120
+ img_urls = get_image_urls(url, pattern=pattern, same_domain=same_domain)
130
121
 
131
122
  if not img_urls:
132
- click.secho("No image URLs found", fg='yellow')
123
+ click.secho("No image URLs found", fg="yellow")
133
124
  sys.exit(0)
134
125
 
135
- click.secho(f"Found {len(img_urls)} image URLs", fg='green')
126
+ click.secho(f"Found {len(img_urls)} image URLs", fg="green")
136
127
 
137
128
  if output:
138
129
  output_path = Path(output)
139
130
  output_path.parent.mkdir(parents=True, exist_ok=True)
140
- with open(output_path, 'w') as f:
141
- f.write('\n'.join(img_urls))
131
+ with open(output_path, "w") as f:
132
+ f.write("\n".join(img_urls))
142
133
  click.echo(f"Image URLs saved to: {output_path}")
143
134
  else:
144
135
  click.echo()
@@ -148,36 +139,34 @@ def get_image_urls_cmd(url, pattern, same_domain, output):
148
139
  sys.exit(0)
149
140
 
150
141
  except Exception as e:
151
- click.secho(f"ERROR: {e}", fg='red', err=True)
142
+ click.secho(f"ERROR: {e}", fg="red", err=True)
152
143
  sys.exit(1)
153
144
 
154
145
 
155
146
  @web.command()
156
- @click.argument('url')
147
+ @click.argument("url")
157
148
  @click.option(
158
- '--output', '-o',
149
+ "--output",
150
+ "-o",
159
151
  type=click.Path(),
160
- help='Output directory (default: $SCITEX_WEB_DOWNLOADS_DIR or $SCITEX_DIR/web/downloads)'
152
+ help="Output directory (default: $SCITEX_WEB_DOWNLOADS_DIR or $SCITEX_DIR/web/downloads)",
161
153
  )
162
154
  @click.option(
163
- '--pattern', '-p',
164
- help='Regex pattern to filter image URLs (e.g., "\\.jpg$")'
155
+ "--pattern", "-p", help='Regex pattern to filter image URLs (e.g., "\\.jpg$")'
165
156
  )
166
157
  @click.option(
167
- '--min-size',
168
- default='100x100',
169
- help='Minimum image size as WIDTHxHEIGHT (default: 100x100)'
158
+ "--min-size",
159
+ default="100x100",
160
+ help="Minimum image size as WIDTHxHEIGHT (default: 100x100)",
170
161
  )
171
162
  @click.option(
172
- '--same-domain',
173
- is_flag=True,
174
- help='Only download images from the same domain'
163
+ "--same-domain", is_flag=True, help="Only download images from the same domain"
175
164
  )
176
165
  @click.option(
177
- '--max-workers',
166
+ "--max-workers",
178
167
  type=int,
179
168
  default=5,
180
- help='Number of concurrent download threads (default: 5)'
169
+ help="Number of concurrent download threads (default: 5)",
181
170
  )
182
171
  def download_images_cmd(url, output, pattern, min_size, same_domain, max_workers):
183
172
  """
@@ -202,13 +191,13 @@ def download_images_cmd(url, output, pattern, min_size, same_domain, max_workers
202
191
  min_size_tuple = None
203
192
  if min_size:
204
193
  try:
205
- width, height = map(int, min_size.split('x'))
194
+ width, height = map(int, min_size.split("x"))
206
195
  min_size_tuple = (width, height)
207
196
  except ValueError:
208
197
  click.secho(
209
198
  f"ERROR: Invalid min-size format. Use WIDTHxHEIGHT (e.g., '100x100')",
210
- fg='red',
211
- err=True
199
+ fg="red",
200
+ err=True,
212
201
  )
213
202
  sys.exit(1)
214
203
 
@@ -218,11 +207,11 @@ def download_images_cmd(url, output, pattern, min_size, same_domain, max_workers
218
207
  pattern=pattern,
219
208
  min_size=min_size_tuple,
220
209
  max_workers=max_workers,
221
- same_domain=same_domain
210
+ same_domain=same_domain,
222
211
  )
223
212
 
224
213
  if not paths:
225
- click.secho("No images downloaded", fg='yellow')
214
+ click.secho("No images downloaded", fg="yellow")
226
215
  sys.exit(0)
227
216
 
228
217
  # Show where images were saved (get actual directory from first path)
@@ -231,37 +220,34 @@ def download_images_cmd(url, output, pattern, min_size, same_domain, max_workers
231
220
  else:
232
221
  actual_output = output or _get_default_download_dir()
233
222
 
234
- click.secho(f"Successfully downloaded {len(paths)} images", fg='green')
223
+ click.secho(f"Successfully downloaded {len(paths)} images", fg="green")
235
224
  click.echo(f"Images saved to: {actual_output}")
236
225
 
237
226
  sys.exit(0)
238
227
 
239
228
  except Exception as e:
240
- click.secho(f"ERROR: {e}", fg='red', err=True)
229
+ click.secho(f"ERROR: {e}", fg="red", err=True)
241
230
  sys.exit(1)
242
231
 
243
232
 
244
233
  @web.command()
245
- @click.argument('url')
234
+ @click.argument("url")
246
235
  @click.option(
247
- '--output', '-o',
236
+ "--output",
237
+ "-o",
248
238
  type=click.Path(),
249
- help='Output directory for the screenshot (default: ~/.scitex/capture)'
239
+ help="Output directory for the screenshot (default: ~/.scitex/capture)",
250
240
  )
251
241
  @click.option(
252
- '--message', '-m',
253
- help='Optional message to include in the screenshot filename'
242
+ "--message", "-m", help="Optional message to include in the screenshot filename"
254
243
  )
255
244
  @click.option(
256
- '--quality', '-q',
257
- type=int,
258
- default=85,
259
- help='JPEG quality 1-100 (default: 85)'
245
+ "--quality", "-q", type=int, default=85, help="JPEG quality 1-100 (default: 85)"
260
246
  )
261
247
  @click.option(
262
- '--full-page',
248
+ "--full-page",
263
249
  is_flag=True,
264
- help='Capture the full page (scrolling) instead of just viewport'
250
+ help="Capture the full page (scrolling) instead of just viewport",
265
251
  )
266
252
  def take_screenshot_cmd(url, output, message, quality, full_page):
267
253
  """
@@ -309,11 +295,7 @@ def take_screenshot_cmd(url, output, message, quality, full_page):
309
295
 
310
296
  # Use playwright MCP server to take screenshot
311
297
  # We'll use a simple approach: navigate to URL and take screenshot
312
- cmd = [
313
- 'playwright', 'screenshot',
314
- url,
315
- str(output_file)
316
- ]
298
+ cmd = ["playwright", "screenshot", url, str(output_file)]
317
299
 
318
300
  # Try using the MCP approach first, fall back to direct playwright if available
319
301
  try:
@@ -329,15 +311,18 @@ def take_screenshot_cmd(url, output, message, quality, full_page):
329
311
  await page.screenshot(
330
312
  path=str(output_file),
331
313
  full_page=full_page,
332
- type='png' if str(output_file).endswith('.png') else 'jpeg',
333
- quality=quality if str(output_file).endswith('.jpg') or str(output_file).endswith('.jpeg') else None
314
+ type="png" if str(output_file).endswith(".png") else "jpeg",
315
+ quality=quality
316
+ if str(output_file).endswith(".jpg")
317
+ or str(output_file).endswith(".jpeg")
318
+ else None,
334
319
  )
335
320
  await browser.close()
336
321
 
337
322
  asyncio.run(capture())
338
323
 
339
324
  if output_file.exists():
340
- click.secho(f"Screenshot saved successfully", fg='green')
325
+ click.secho(f"Screenshot saved successfully", fg="green")
341
326
  click.echo(f"Location: {output_file}")
342
327
  sys.exit(0)
343
328
  else:
@@ -345,15 +330,17 @@ def take_screenshot_cmd(url, output, message, quality, full_page):
345
330
 
346
331
  except ImportError:
347
332
  # Fall back to using playwright CLI if the Python package is not available
348
- click.secho("Playwright Python package not found, trying CLI...", fg='yellow')
333
+ click.secho(
334
+ "Playwright Python package not found, trying CLI...", fg="yellow"
335
+ )
349
336
  result = subprocess.run(
350
- ['playwright', 'screenshot', url, str(output_file)],
337
+ ["playwright", "screenshot", url, str(output_file)],
351
338
  capture_output=True,
352
- text=True
339
+ text=True,
353
340
  )
354
341
 
355
342
  if result.returncode == 0 and output_file.exists():
356
- click.secho(f"Screenshot saved successfully", fg='green')
343
+ click.secho(f"Screenshot saved successfully", fg="green")
357
344
  click.echo(f"Location: {output_file}")
358
345
  sys.exit(0)
359
346
  else:
@@ -361,17 +348,24 @@ def take_screenshot_cmd(url, output, message, quality, full_page):
361
348
 
362
349
  except Exception as e:
363
350
  error_msg = str(e)
364
- click.secho(f"ERROR: {error_msg}", fg='red', err=True)
351
+ click.secho(f"ERROR: {error_msg}", fg="red", err=True)
365
352
  click.echo()
366
353
 
367
354
  # Provide context-specific troubleshooting
368
355
  if "ERR_CONNECTION_REFUSED" in error_msg or "Connection refused" in error_msg:
369
356
  click.echo("Troubleshooting - Connection Refused:")
370
357
  click.echo(" 1. Make sure a web server is running at the specified URL")
371
- click.echo(" 2. Check if the port is correct (e.g., http://127.0.0.1:8000/)")
358
+ click.echo(
359
+ " 2. Check if the port is correct (e.g., http://127.0.0.1:8000/)"
360
+ )
372
361
  click.echo(" 3. Verify the server is accessible: curl <url>")
373
- click.echo(" 4. If using WSL, you may need to use the WSL IP instead of 127.0.0.1")
374
- elif "ERR_NAME_NOT_RESOLVED" in error_msg or "Name or service not known" in error_msg:
362
+ click.echo(
363
+ " 4. If using WSL, you may need to use the WSL IP instead of 127.0.0.1"
364
+ )
365
+ elif (
366
+ "ERR_NAME_NOT_RESOLVED" in error_msg
367
+ or "Name or service not known" in error_msg
368
+ ):
375
369
  click.echo("Troubleshooting - DNS Resolution Failed:")
376
370
  click.echo(" 1. Check if the domain name is correct")
377
371
  click.echo(" 2. Verify internet connection")
@@ -385,7 +379,10 @@ def take_screenshot_cmd(url, output, message, quality, full_page):
385
379
  click.echo("Troubleshooting - Playwright Not Installed:")
386
380
  click.echo(" 1. Install Playwright: pip install playwright")
387
381
  click.echo(" 2. Install browsers: playwright install chromium")
388
- elif "Executable doesn't exist" in error_msg or "browser executable" in error_msg.lower():
382
+ elif (
383
+ "Executable doesn't exist" in error_msg
384
+ or "browser executable" in error_msg.lower()
385
+ ):
389
386
  click.echo("Troubleshooting - Browser Not Installed:")
390
387
  click.echo(" 1. Install Chromium browser: playwright install chromium")
391
388
  click.echo(" 2. Or install all browsers: playwright install")
@@ -399,11 +396,11 @@ def take_screenshot_cmd(url, output, message, quality, full_page):
399
396
 
400
397
 
401
398
  # Register command aliases
402
- web.add_command(get_urls_cmd, name='get-urls')
403
- web.add_command(get_image_urls_cmd, name='get-image-urls')
404
- web.add_command(download_images_cmd, name='download-images')
405
- web.add_command(take_screenshot_cmd, name='take-screenshot')
399
+ web.add_command(get_urls_cmd, name="get-urls")
400
+ web.add_command(get_image_urls_cmd, name="get-image-urls")
401
+ web.add_command(download_images_cmd, name="download-images")
402
+ web.add_command(take_screenshot_cmd, name="take-screenshot")
406
403
 
407
404
 
408
- if __name__ == '__main__':
405
+ if __name__ == "__main__":
409
406
  web()
scitex/cli/writer.py CHANGED
@@ -11,7 +11,7 @@ import sys
11
11
  from pathlib import Path
12
12
 
13
13
 
14
- @click.group(context_settings={'help_option_names': ['-h', '--help']})
14
+ @click.group(context_settings={"help_option_names": ["-h", "--help"]})
15
15
  def writer():
16
16
  """
17
17
  Manuscript writing and LaTeX compilation
@@ -27,21 +27,16 @@ def writer():
27
27
 
28
28
 
29
29
  @writer.command()
30
- @click.argument('project_dir', type=click.Path())
30
+ @click.argument("project_dir", type=click.Path())
31
31
  @click.option(
32
- '--git-strategy', '-g',
33
- type=click.Choice(['child', 'parent', 'origin', 'none'], case_sensitive=False),
34
- default='child',
35
- help='Git initialization strategy (default: child)'
36
- )
37
- @click.option(
38
- '--branch', '-b',
39
- help='Specific branch of template to clone'
40
- )
41
- @click.option(
42
- '--tag', '-t',
43
- help='Specific tag/release of template to clone'
32
+ "--git-strategy",
33
+ "-g",
34
+ type=click.Choice(["child", "parent", "origin", "none"], case_sensitive=False),
35
+ default="child",
36
+ help="Git initialization strategy (default: child)",
44
37
  )
38
+ @click.option("--branch", "-b", help="Specific branch of template to clone")
39
+ @click.option("--tag", "-t", help="Specific tag/release of template to clone")
45
40
  def clone(project_dir, git_strategy, branch, tag):
46
41
  """
47
42
  Clone a new writer project from template
@@ -74,7 +69,7 @@ def clone(project_dir, git_strategy, branch, tag):
74
69
  sys.exit(1)
75
70
 
76
71
  # Convert git_strategy 'none' to None
77
- if git_strategy and git_strategy.lower() == 'none':
72
+ if git_strategy and git_strategy.lower() == "none":
78
73
  git_strategy = None
79
74
 
80
75
  click.echo(f"Cloning writer project: {project_dir}")
@@ -90,11 +85,16 @@ def clone(project_dir, git_strategy, branch, tag):
90
85
  if result:
91
86
  project_path = Path(project_dir)
92
87
  click.echo()
93
- click.secho(f"✓ Successfully cloned project at {project_path.absolute()}", fg='green')
88
+ click.secho(
89
+ f"✓ Successfully cloned project at {project_path.absolute()}",
90
+ fg="green",
91
+ )
94
92
  click.echo()
95
93
  click.echo("Project structure:")
96
94
  click.echo(f" {project_dir}/")
97
- click.echo(f" ├── 00_shared/ # Shared resources (figures, bibliography)")
95
+ click.echo(
96
+ f" ├── 00_shared/ # Shared resources (figures, bibliography)"
97
+ )
98
98
  click.echo(f" ├── 01_manuscript/ # Main manuscript")
99
99
  click.echo(f" ├── 02_supplementary/ # Supplementary materials")
100
100
  click.echo(f" ├── 03_revision/ # Revision documents")
@@ -105,35 +105,36 @@ def clone(project_dir, git_strategy, branch, tag):
105
105
  click.echo(f" # Edit your manuscript in 01_manuscript/contents/")
106
106
  click.echo(f" scitex writer compile manuscript")
107
107
  else:
108
- click.secho(f"✗ Failed to clone project", fg='red', err=True)
108
+ click.secho(f"✗ Failed to clone project", fg="red", err=True)
109
109
  sys.exit(1)
110
110
 
111
111
  except Exception as e:
112
- click.secho(f"Error: {e}", fg='red', err=True)
112
+ click.secho(f"Error: {e}", fg="red", err=True)
113
113
  sys.exit(1)
114
114
 
115
115
 
116
116
  @writer.command()
117
117
  @click.argument(
118
- 'document',
119
- type=click.Choice(['manuscript', 'supplementary', 'revision'], case_sensitive=False),
120
- default='manuscript'
118
+ "document",
119
+ type=click.Choice(
120
+ ["manuscript", "supplementary", "revision"], case_sensitive=False
121
+ ),
122
+ default="manuscript",
121
123
  )
122
124
  @click.option(
123
- '--dir', '-d',
125
+ "--dir",
126
+ "-d",
124
127
  type=click.Path(exists=True),
125
- help='Project directory (defaults to current directory)'
128
+ help="Project directory (defaults to current directory)",
126
129
  )
127
130
  @click.option(
128
- '--track-changes',
129
- is_flag=True,
130
- help='Enable change tracking (revision only)'
131
+ "--track-changes", is_flag=True, help="Enable change tracking (revision only)"
131
132
  )
132
133
  @click.option(
133
- '--timeout',
134
+ "--timeout",
134
135
  type=int,
135
136
  default=300,
136
- help='Compilation timeout in seconds (default: 300)'
137
+ help="Compilation timeout in seconds (default: 300)",
137
138
  )
138
139
  def compile(document, dir, track_changes, timeout):
139
140
  """
@@ -160,21 +161,24 @@ def compile(document, dir, track_changes, timeout):
160
161
  click.echo()
161
162
 
162
163
  # Compile based on document type
163
- if document == 'manuscript':
164
+ if document == "manuscript":
164
165
  result = writer.compile_manuscript(timeout=timeout)
165
- elif document == 'supplementary':
166
+ elif document == "supplementary":
166
167
  result = writer.compile_supplementary(timeout=timeout)
167
- elif document == 'revision':
168
+ elif document == "revision":
168
169
  result = writer.compile_revision(
169
- track_changes=track_changes,
170
- timeout=timeout
170
+ track_changes=track_changes, timeout=timeout
171
171
  )
172
172
 
173
173
  if result.success:
174
- click.secho(f"✓ Compilation successful!", fg='green')
174
+ click.secho(f"✓ Compilation successful!", fg="green")
175
175
  click.echo(f"PDF: {result.output_pdf}")
176
176
  else:
177
- click.secho(f"✗ Compilation failed (exit code {result.exit_code})", fg='red', err=True)
177
+ click.secho(
178
+ f"✗ Compilation failed (exit code {result.exit_code})",
179
+ fg="red",
180
+ err=True,
181
+ )
178
182
  if result.errors:
179
183
  click.echo()
180
184
  click.echo("Errors:")
@@ -183,15 +187,16 @@ def compile(document, dir, track_changes, timeout):
183
187
  sys.exit(result.exit_code)
184
188
 
185
189
  except Exception as e:
186
- click.secho(f"Error: {e}", fg='red', err=True)
190
+ click.secho(f"Error: {e}", fg="red", err=True)
187
191
  sys.exit(1)
188
192
 
189
193
 
190
194
  @writer.command()
191
195
  @click.option(
192
- '--dir', '-d',
196
+ "--dir",
197
+ "-d",
193
198
  type=click.Path(exists=True),
194
- help='Project directory (defaults to current directory)'
199
+ help="Project directory (defaults to current directory)",
195
200
  )
196
201
  def info(dir):
197
202
  """
@@ -220,23 +225,24 @@ def info(dir):
220
225
 
221
226
  # Check for compiled PDFs
222
227
  click.echo("Compiled PDFs:")
223
- for doc_type in ['manuscript', 'supplementary', 'revision']:
228
+ for doc_type in ["manuscript", "supplementary", "revision"]:
224
229
  pdf = writer.get_pdf(doc_type)
225
230
  if pdf:
226
- click.secho(f" ✓ {doc_type}: {pdf}", fg='green')
231
+ click.secho(f" ✓ {doc_type}: {pdf}", fg="green")
227
232
  else:
228
233
  click.echo(f" - {doc_type}: not compiled")
229
234
 
230
235
  except Exception as e:
231
- click.secho(f"Error: {e}", fg='red', err=True)
236
+ click.secho(f"Error: {e}", fg="red", err=True)
232
237
  sys.exit(1)
233
238
 
234
239
 
235
240
  @writer.command()
236
241
  @click.option(
237
- '--dir', '-d',
242
+ "--dir",
243
+ "-d",
238
244
  type=click.Path(exists=True),
239
- help='Project directory (defaults to current directory)'
245
+ help="Project directory (defaults to current directory)",
240
246
  )
241
247
  def watch(dir):
242
248
  """
@@ -263,7 +269,7 @@ def watch(dir):
263
269
  click.echo()
264
270
  click.echo("Stopped watching")
265
271
  except Exception as e:
266
- click.secho(f"Error: {e}", fg='red', err=True)
272
+ click.secho(f"Error: {e}", fg="red", err=True)
267
273
  sys.exit(1)
268
274
 
269
275
 
scitex/cloud/__init__.py CHANGED
@@ -12,21 +12,23 @@ from typing import Optional
12
12
 
13
13
  def is_cloud_environment() -> bool:
14
14
  """Check if running in SciTeX Cloud environment."""
15
- return os.environ.get('SCITEX_CLOUD_CODE_WORKSPACE') == 'true'
15
+ return os.environ.get("SCITEX_CLOUD_CODE_WORKSPACE") == "true"
16
16
 
17
17
 
18
18
  def get_cloud_backend() -> str:
19
19
  """Get the cloud backend type."""
20
- return os.environ.get('SCITEX_CLOUD_CODE_BACKEND', 'default')
20
+ return os.environ.get("SCITEX_CLOUD_CODE_BACKEND", "default")
21
21
 
22
22
 
23
23
  def get_project_root() -> Optional[Path]:
24
24
  """Get the project root directory."""
25
- project_root = os.environ.get('SCITEX_CLOUD_CODE_PROJECT_ROOT')
25
+ project_root = os.environ.get("SCITEX_CLOUD_CODE_PROJECT_ROOT")
26
26
  return Path(project_root) if project_root else None
27
27
 
28
28
 
29
- def emit_inline_image(image_path: str, alt_text: str = "Figure", width: int = 600) -> None:
29
+ def emit_inline_image(
30
+ image_path: str, alt_text: str = "Figure", width: int = 600
31
+ ) -> None:
30
32
  """
31
33
  Emit inline image marker for terminal display using iTerm2 protocol.
32
34
 
@@ -45,7 +47,7 @@ def emit_inline_image(image_path: str, alt_text: str = "Figure", width: int = 60
45
47
  return
46
48
 
47
49
  backend = get_cloud_backend()
48
- if backend != 'inline':
50
+ if backend != "inline":
49
51
  return
50
52
 
51
53
  # Convert to absolute path if relative
@@ -73,11 +75,12 @@ def emit_inline_image(image_path: str, alt_text: str = "Figure", width: int = 60
73
75
  display_path = image_path
74
76
 
75
77
  # Emit marker that terminal consumer will detect
76
- print(f'\n[SCITEX_IMAGE:{display_path}:{width}:{alt_text}]\n', flush=True)
78
+ print(f"\n[SCITEX_IMAGE:{display_path}:{width}:{alt_text}]\n", flush=True)
77
79
 
78
80
  except Exception as e:
79
81
  print(f"Error displaying inline image: {e}", file=sys.stderr)
80
82
  import traceback
83
+
81
84
  traceback.print_exc(file=sys.stderr)
82
85
 
83
86
 
@@ -113,11 +116,11 @@ def emit_file_link(file_path: str, line_number: Optional[int] = None) -> None:
113
116
 
114
117
 
115
118
  __all__ = [
116
- 'is_cloud_environment',
117
- 'get_cloud_backend',
118
- 'get_project_root',
119
- 'emit_inline_image',
120
- 'emit_file_link',
119
+ "is_cloud_environment",
120
+ "get_cloud_backend",
121
+ "get_project_root",
122
+ "emit_inline_image",
123
+ "emit_file_link",
121
124
  ]
122
125
 
123
126
  # Auto-import matplotlib hook to enable inline plotting